Built-in Keyboard and Trackpad not Working After Logic Board Swap

Hi, so I have been repairing computers for my family for a while so this is extra frustrating to me. Trying to fix one macbook pro, couldn't tell if it was the keyboard or the logic board, so I removed the logic board and put it in a laptop where everything was working properly (no issues). Was able to turn on the laptop after the logic board swap, and so I put the original logic board back in the known good laptop and thought that would be that, but no the machine had other plans for me...

The keyboard and the trackpad are now not being recognized by the laptop! Connecting a USB mouse and keyboard allows me to log in and see that everything else appears to be fine. However, what is really maddening/puzzling is that on top of the power button still working, I reset the PRAM AND the SMC with the built-in keyboard and in BOTH cases, that worked.

When I did the keyboard combination for resetting the PRAM, the laptop rebooted again, and made the chime a second time, and when I reset the SMC, the battery indicator light briefly flashed a different colour. So, how can the keyboard work for those multiple key combinations but typing one letter at a time does nothing?

Of course I tried reseating the keyboard cable several times, but the trackpad is really puzzling because its connector is just a socket, so it plugs in quite easily. Also, to answer your obvious question, no there appears to be no damage to these connectors, I even looked with a magnifying glass. Only indication I have in OS X that something is amiss is when I go to "Accessibility" in System Preferences and click on keyboard, the top option to use "F1, F2 etc as regular function keys keeps appearing and disappearing every second, alternating back and forth, back and forth.

Other than that, if I use USB keyboard and mouse I can use the laptop normally. Please help, I feel like such an idiot, both of these laptops are out of warranty. Thank you.